Tuesday, October 1

Another productive day! I started off by doing some FISH 250 stuff and updating some of the class sheets. After that, I moved on to my AFS chapter - I got my last set of edits back, so spent a good portion of the day chatting about that, reflecting on the edits, and updating the chapter accordingly.

After that, time to move on to the modeling paper! Last time, I rewrote the whole abstract and intro. That meant it was time to move on to the methods! I did a bunch of work on the various comments in the methods, along with clearing up a number of the relatively quick and easy edits in the results and discussion. After that, I started tackling the bigger stuff. First on the list: remake my first figure. It really needs a total redo - the mapping package I used when I originally created it is just totally inadequate, and doesn’t have the level of detail necessary. I decided to switch over to ggmap, following this guide. However, in order to do so, I needed to install a ton of R packages - after all, I’m working off a fresh Linux install! Kept getting error after error, as I was missing a whole bunch of compilers. Had a bit of a cycle for a while - get an error installing the R package, go install the compiler, successfully install the package, get an error installing the next R package.

I also got around to migrating my blog over from the Bittercrab Wordpress site to Substack. The Bittercrab site felt, unsurprisingly, very tied to bitter crab research, and I’m wanting to write about a wider array of topics. I came up with the name Aligned Reads, which I’m very proud of. Anyways, I spent a good chunk of time copying over my old blog posts, setting up the site, et cetera!

Wednesday, October 2nd

More progress! I spent today on a mix of logistical issues and thesis work.

Logistical issues:

  • Sorted out funding for oSTEM trip
  • Bought tickets for Amtrak (for oSTEM trip)
  • Messaged Sam and Steven about getting First Aid training and the logistics thereof

Misc issues:

  • Read through AFS chapter one more time

Thesis work:

Completely redid Figure 1! Previously, it was a frankly pretty crappy map showing Tanner crab infection rates by location. I redid it from scratch. Some changes:

  • Used a much more detailed and beautiful Stadia map.
  • Changed it from showing infection to showing survey (Tanner vs RKC survey)
  • Added shapes to represent the two surveys
  • Added a zoomed-out map in the corner showing Alaska more generally
  • Put a box in the zoomed-out Alaska map showing the area this map focuses on
  • Put a border around the zoomed-out map in the corner

This last step gave me absolute fits, as there’s some weird buffering going on with draw_line() in the cowplot package - the coordinates (0,0) don’t correspond to the bottom left corner, but instead to somewhere even further left and lower. But it wasn’t being consistently interpreted by the mapping function, which was the absolute worst. So (forgive me Steven), I used Gimp to throw a dashed border around the corner map.

Anyways, productive day. Now off to my self-criticism session in which I’ll be held accountable for drawing that border and thus violating reproducibility principles! If I don’t post again, you know what happened to me.

Thursday, October 3rd

Well, Thursdays are my chaotic day - got two labs to TA back-to-back! Both went great, but since I was teaching from 8:30-4:30, I didn’t have much time or energy to work on non-TAing stuff. Did accomplish a few things though!

  • Sent in AFS chapter!!!!
  • Set up appointment to get First Aid cert, and got it booked by Sam so no reimbursement things to deal with!
  • Submitted TREQ request for reimbursement for oSTEM trip
  • Graded all the late papers for FISH 250 Lab 1
  • Made a teensy bit of progress reading through Linux book

Friday, October 4th

Filled in for Celeste’s 250 lab today, so most of the day was that! Beyond that, I did the following:

  • Sorted out a bunch of TREQ issues re: reimbursement
  • Got in touch with TREQ to updat emy name in their system

Sunday, October 6th

Came in after a lil Quaker meeting to get some stuff done (also got an oyster knife from the meeting, neat!). Good news: I ended up going through all of the paper edits from Chelsea!!! Yay, yippee, go Aspen!!!

Monday, October 7th

First lab meeting of the new quarter! Fun times and good vibes were had by all

Had office hours + lab meeting + FISH 250 meeting today, so haven’t had a bunch of time. However, I was able to get Figure 2 figured out!!! R was giving me fits, I couldn’t for the life of me figure out how to turn a model summary table into a regular table - none of the usual functions are built for an object of class “summary.averaging”. Turns out, I just had to create the summary and then specify the full coefficient matrix (coefmat.full).

Anyways, once I did that, it was pretty simple to create the figure!

Current question: should I sort the predictor variables (y-axis) based on alphabetical order, or based on absolute value of the estimated coefficient?

Update: figured that out, I’ll base them on absolute value! I also decided to eliminate the intercept variable.

I continued on, and created plots for the male-specific and female-specific models! However, they’d look cleaner if they were incorporated together as a single figure (with a shared axis?)

Also, cannot BELIEVE I never thought of working in the line “but why male models?” somewhere into my paper when discussing the existence of my male-specific models. Ah well, even the most beautiful puns fade into dust

I also made some small changes to my website - added a link to Aligned Reads, etc.

Tuesday, October 8th

No work today - got a small medical procedure done on my toe. Between that and getting my COVID and flu shots Monday afternoon, I was out of commission all day. Still, a restful day in bed! Movie recommendation of the day: “Los Tallos Amargos” (The Bitter Stems). Mid-50s Argentinean noir - delightfully tense and full of twists. Great way to spend the day (thanks, Scarecrow Video!)

Wednesday, October 9th

Spent the morning at the UW career fair, and the afternoon working on my graphs. Made some important changes, including the following:

  • Got some feedback (thanks, Ariana!) and decided on two figures. Figure 2 would be just the general model coefficients, while Figure 3 would be the sex-specific models
  • Created both those figures
  • Edited figures so that significant coefficients were plotted in black, and non-significant coefficients in grey.
  • Played around some with sizing and captions
  • Went through a piece Niamh is writing about my modeling research and made sure everything was shipshape
  • Did some office hours and things of that nature

Thursday, October 10th

It’s Thursday, so it’s teaching lab day! Couldn’t get much lab work done, of course. But I did get through a few dozen pages of the Linux book (taking very detailed notes!) and scheduled a meeting with Steven for tomorrow!

Once I’d eaten my academic veggies, I also got started on another post for Aligned Reads on thinking like a scientist (and why it’s not always great). Fun to write, really love being able to articulate these thoughts and turn them from something abstract to something more concrete.

Friday, October 11th

Spent most of the day in a First Aid class! Learned a bunch, and got my First Aid/CPR cert (required for TAing). Aside from that, had a meeting with Steven, and sent an email out establishing my plans to him and Chelsea.

A brief summary

  • Complete the modeling paper (get edits, do supplemental tables, submit)

  • Complete the gene expression paper (correct edits, submit)

  • Get both papers formatted for thesis

  • Schedule presentation

  • Present and graduate!

Saturday, October 12th

Finished my Aligned Reads post! Was v fun to write, a great time. I also started on some grading!

Sunday, October 13th

Worked on grading for the first FISH 250 lab! It’s definitely a slow one, but getting through it bit by bit

Up next:

  • Continue reading Linux book
  • Schedule committee meeting